I think the main thing is to think about how the skills can remain interesting over time. I imagine the game will be similar in structure to previous outings, which means that it'll allow for around 100 levels per character. If so, there needs to be something interesting that happens to the skills as you upgrade them other than just increasing numbers. This problem is exacerbated by the fact that you have all skills unlocked from the start, meaning that players just choose what they want right away and never diversify.
One thing Drox did very well is give you different skill options over time. I'd love to see some of that influence a DC-style skill system.
Here's an idea to reduce the burden of having to not only design many skills, but also needing to design many skills over time: plant random modifications of skills every X levels. You could design random bonuses that modify skills, and which are randomly assigned to skills every X (say, 5) levels. So a fireball could get some extra cold damage, or double (2 fireballs), or get reduced cooldown etc. This is similar to D3's rune system, but doesn't have to be nearly as complex, and can't be manipulated by the player. Some of these modifications could even have a cost e.g. slower spell but more powerful. This would make a player reconsider that spell and perhaps prefer another one instead.
The other thing to watch out for is linear spell damage vs damage locked to items. Honestly, even Blizzard gave up on balancing spell damage vs item damage, and the thing to do is probably just have spell damage scale with weapon damage (preferably off of some 'minor' stat that's not the same as damage but is useless to fighters). In my DC mod, I think I eventually settled on resistances being the main stat to modify spell damage, and I think this ended up being pretty cool. This way, different magic disciplines relied on different resistances and items became cool again for mages of all types.